pdb
PDB parsing class
This module parses PDBs in accordance to PDB Format Description Version 2.2 (1996); it is not very forgiving. Each class in this module corresponds to a record in the PDB Format Description. Much of the documentation for the classes is taken directly from the above PDB Format Description.
Code author: Todd Dolinsky
Code author: Yong Huang
Code author: Nathan Baker
- class pdb2pqr.pdb.ANISOU(line)[source]
ANISOU class
The ANISOU records present the anisotropic temperature factors.
- __init__(line)[source]
Initialize by parsing line:
COLUMNS
TYPE
FIELD
DEFINITION
7-11
int
serial
Atom serial number.
13-16
string
name
Atom name.
17
string
alt_loc
Alternate location indicator.
18-20
string
res_name
Residue name.
22
string
chain_id
Chain identifier.
23-26
int
res_seq
Residue sequence number.
27
string
ins_code
Insertion code.
29-35
int
u00
U(1,1)
36-42
int
u11
U(2,2)
43-49
int
u22
U(3,3)
50-56
int
u01
U(1,2)
57-63
int
u02
U(1,3)
64-70
int
u12
U(2,3)
73-76
string
seg_id
Segment identifier, left-justified.
77-78
string
element
Element symbol, right-justified.
79-80
string
charge
Charge on the atom.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.ATOM(line)[source]
ATOM class
The ATOM records present the atomic coordinates for standard residues. They also present the occupancy and temperature factor for each atom. Heterogen coordinates use the HETATM record type. The element symbol is always present on each ATOM record; segment identifier and charge are optional.
- __init__(line)[source]
Initialize by parsing line
COLUMNS
TYPE
FIELD
DEFINITION
7-11
int
serial
Atom serial number.
13-16
string
name
Atom name.
17
string
alt_loc
Alternate location indicator.
18-20
string
res_name
Residue name.
22
string
chain_id
Chain identifier.
23-26
int
res_seq
Residue sequence number.
27
string
ins_code
Code for insertion of residues.
31-38
float
x
Orthogonal coordinates for X in Angstroms.
39-46
float
y
Orthogonal coordinates for Y in Angstroms.
47-54
float
z
Orthogonal coordinates for Z in Angstroms.
55-60
float
occupancy
Occupancy.
61-66
float
temp_factor
Temperature factor.
73-76
string
seg_id
Segment identifier, left-justified.
77-78
string
element
Element symbol, right-justified.
79-80
string
charge
Charge on the atom.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.AUTHOR(line)[source]
AUTHOR field
The AUTHOR record contains the names of the people responsible for the contents of the entry.
- class pdb2pqr.pdb.BaseRecord(line)[source]
Base class for all records.
Verifies the received record type.
- class pdb2pqr.pdb.CAVEAT(line)[source]
CAVEAT field
CAVEAT warns of severe errors in an entry. Use caution when using an entry containing this record.
- class pdb2pqr.pdb.CISPEP(line)[source]
CISPEP field
CISPEP records specify the prolines and other peptides found to be in the cis conformation. This record replaces the use of footnote records to list cis peptides.
- __init__(line)[source]
Initialize by parsing line
COLUMNS
TYPE
FIELD
DEFINITION
8-10
int
ser_num
Record serial number.
12-14
string
pep1
Residue name.
16
string
chain_id1
Chain identifier.
18-21
int
seq_num1
Residue sequence number.
22
string
icode1
Insertion code.
26-28
string
pep2
Residue name.
30
string
chain_id2
Chain identifier.
32-35
int
seq_num2
Residue sequence number.
36
string
icode2
Insertion code.
44-46
int
mod_num
Identifies the specific model.
54-59
float
measure
Measure of the angle in degrees.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.COMPND(line)[source]
COMPND field
The COMPND record describes the macromolecular contents of an entry. Each macromolecule found in the entry is described by a set of token: value pairs, and is referred to as a COMPND record component. Since the concept of a molecule is difficult to specify exactly, PDB staff may exercise editorial judgment in consultation with depositors in assigning these names.
For each macromolecular component, the molecule name, synonyms, number assigned by the Enzyme Commission (EC), and other relevant details are specified.
- class pdb2pqr.pdb.CONECT(line)[source]
CONECT class
The CONECT records specify connectivity between atoms for which coordinates are supplied. The connectivity is described using the atom serial number as found in the entry. CONECT records are mandatory for HET groups (excluding water) and for other bonds not specified in the standard residue connectivity table which involve atoms in standard residues (see Appendix 4 for the list of standard residues). These records are generated by the PDB.
- __init__(line)[source]
Initialize by parsing line
COLUMNS
TYPE
FIELD
DEFINITION
7-11
int
serial
Atom serial number
12-16
int
serial1
Serial number of bonded atom
17-21
int
serial2
Serial number of bonded atom
22-26
int
serial3
Serial number of bonded atom
27-31
int
serial4
Serial number of bonded atom
32-36
int
serial5
Serial number of hydrogen bonded atom
37-41
int
serial6
Serial number of hydrogen bonded atom
42-46
int
serial7
Serial number of salt bridged atom
47-51
int
serial8
Serial number of hydrogen bonded atom
52-56
int
serial9
Serial number of hydrogen bonded atom
57-61
int
serial10
Serial number of salt bridged atom
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.CRYST1(line)[source]
CRYST1 class
The CRYST1 record presents the unit cell parameters, space group, and Z value. If the structure was not determined by crystallographic means, CRYST1 simply defines a unit cube.
- __init__(line)[source]
Initialize by parsing line
COLUMNS
TYPE
FIELD
DEFINITION
7-15
float
a
a (Angstroms).
16-24
float
b
b (Angstroms).
25-33
float
c
c (Angstroms).
34-40
float
alpha
alpha (degrees).
41-47
float
beta
beta (degrees).
48-54
float
gamma
gamma (degrees).
56-66
string
space_group
Space group.
67-70
int
z
Z value.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.DBREF(line)[source]
DBREF field
The DBREF record provides cross-reference links between PDB sequences and the corresponding database entry or entries. A cross reference to the sequence database is mandatory for each peptide chain with a length greater than ten (10) residues. For nucleic acid entries a DBREF record pointing to the Nucleic Acid Database (NDB) is mandatory when the corresponding entry exists in NDB.
- __init__(line)[source]
Initialize by parsing a line.
COLUMNS
TYPE
FIELD
DEFINITION
8-11
string
id_code
ID code of this entry.
13
string
chain_id
Chain identifier.
15-18
int
seq_begin
Initial sequence number of the PDB sequence segment.
19
string
insert_begin
Initial insertion code of the PDB sequence segment.
21-24
int
seq_end
Ending sequence number of the PDB sequence segment.
25
string
insert_end
Ending insertion code of the PDB sequence segment.
27-32
string
database
Sequence database name. “PDB” when a corresponding sequence database entry has not been identified.
34-41
string
db_accession
Sequence database accession code. For GenBank entries, this is the NCBI gi number.
43-54
string
db_id_code
Sequence database identification code. For GenBank entries, this is the accession code.
56-60
int
db_seq_begin
Initial sequence number of the database seqment.
61
string
db_ins_begin
Insertion code of initial residue of the segment, if PDB is the reference.
63-67
int
dbseq_end
Ending sequence number of the database segment.
68
string
db_ins_end
Insertion code of the ending residue of the segment, if PDB is the reference.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.END(line)[source]
END class
The END records are paired with MODEL records to group individual structures found in a coordinate entry.
- class pdb2pqr.pdb.ENDMDL(line)[source]
ENDMDL class
The ENDMDL records are paired with MODEL records to group individual structures found in a coordinate entry.
- class pdb2pqr.pdb.EXPDTA(line)[source]
EXPDTA field
The EXPDTA record identifies the experimental technique used. This may refer to the type of radiation and sample, or include the spectroscopic or modeling technique. Permitted values include:
ELECTRON DIFFRACTION
FIBER DIFFRACTION
FLUORESCENCE TRANSFER
NEUTRON DIFFRACTION
NMR
THEORETICAL MODEL
X-RAY DIFFRACTION
- class pdb2pqr.pdb.FORMUL(line)[source]
FORMUL field
The FORMUL record presents the chemical formula and charge of a non-standard group.
- class pdb2pqr.pdb.HEADER(line)[source]
HEADER field
The HEADER record uniquely identifies a PDB entry through the id_code field. This record also provides a classification for the entry. Finally, it contains the date the coordinates were deposited at the PDB.
- __init__(line)[source]
Initialize by parsing a line.
COLUMNS
TYPE
FIELD
DEFINITION
11-50
string
classification
Classifies the molecule(s)
51-59
string
dep_date
Deposition date. This is the date the coordinates were received by the PDB
63-66
string
id_code
This identifier is unique wihin within PDB
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.HELIX(line)[source]
HELIX field
HELIX records are used to identify the position of helices in the molecule. Helices are both named and numbered. The residues where the helix begins and ends are noted, as well as the total length.
- __init__(line)[source]
Initialize by parsing line
COLUMNS
TYPE
FIELD
DEFINITION
8-10
int
ser_num
Serial number of the helix. This starts at 1 and increases incrementally.
12-14
string
helix_id
Helix identifier. In addition to a serial number, each helix is given an alphanumeric character helix identifier.
16-18
string
init_res_name
Name of the initial residue.
20
string
init_chain_id
Chain identifier for the chain containing this helix.
22-25
int
init_seq_num
Sequence number of the initial residue.
26
string
init_i_code
Insertion code of the initial residue.
28-30
string
end_res_name
Name of the terminal residue of the helix.
32
string
end_chain_id
Chain identifier for the chain containing this helix.
34-37
int
end_seq_num
Sequence number of the terminal residue.
38
string
end_i_code
Insertion code of the terminal residue.
39-40
int
helix_class
Helix class (see below).
41-70
string
comment
Comment about this helix.
72-76
int
length
Length of this helix.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.HET(line)[source]
HET field
HET records are used to describe non-standard residues, such as prosthetic groups, inhibitors, solvent molecules, and ions for which coordinates are supplied. Groups are considered HET if they are:
not one of the standard amino acids, and
not one of the nucleic acids (C, G, A, T, U, and I), and
not one of the modified versions of nucleic acids (+C, +G, +A, +T, +U, and +I), and
not an unknown amino acid or nucleic acid where UNK is used to indicate the unknown residue name.
Het records also describe heterogens for which the chemical identity is unknown, in which case the group is assigned the hetatm_id UNK.
- __init__(line)[source]
Initialize by parsing line
COLUMNS
TYPE
FIELD
DEFINITION
8-10
string
hetatm_id
Het identifier, right-justified.
13
string
ChainID
Chain identifier.
14-17
int
seq_num
Sequence number.
18
string
ins_code
Insertion code.
21-25
int
num_het_atoms
Number of HETATM records.
31-70
string
text
Text describing Het group.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.HETATM(line, sybyl_type='A.aaa', l_bonds=[], l_bonded_atoms=[])[source]
HETATM class
The HETATM records present the atomic coordinate records for atoms within “non-standard” groups. These records are used for water molecules and atoms presented in HET groups.
- __init__(line, sybyl_type='A.aaa', l_bonds=[], l_bonded_atoms=[])[source]
Initialize by parsing line
COLUMNS
TYPE
FIELD
DEFINITION
7-11
int
serial
Atom serial number.
13-16
string
name
Atom name.
17
string
alt_loc
Alternate location indicator.
18-20
string
res_name
Residue name.
22
string
chain_id
Chain identifier.
23-26
int
res_seq
Residue sequence number.
27
string
ins_code
Code for insertion of residues.
31-38
float
x
Orthogonal coordinates for X in Angstroms.
39-46
float
y
Orthogonal coordinates for Y in Angstroms.
47-54
float
z
Orthogonal coordinates for Z in Angstroms.
55-60
float
occupancy
Occupancy.
61-66
float
temp_factor
Temperature factor.
73-76
string
seg_id
Segment identifier, left- justified.
77-78
string
element
Element symbol, right-justified.
79-80
string
charge
Charge on the atom.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.HETNAM(line)[source]
HETNAM field
This record gives the chemical name of the compound with the given hetatm_id.
- class pdb2pqr.pdb.HETSYN(line)[source]
HETSYN field
This record provides synonyms, if any, for the compound in the corresponding (i.e., same hetatm_id) HETNAM record. This is to allow greater flexibility in searching for HET groups.
- class pdb2pqr.pdb.HYDBND(line)[source]
HYDBND field
The HYDBND records specify hydrogen bonds in the entry.
- __init__(line)[source]
Initialize by parsing line
COLUMNS
TYPE
FIELD
DEFINITION
13-16
string
name1
Atom name.
17
string
alt_loc1
Alternate location indicator.
18-20
string
res_name1
Residue name.
22
string
chain1
Chain identifier.
23-27
int
res_seq1
Residue sequence number.
28
string
i_code1
Insertion code.
30-33
string
name_h
Hydrogen atom name.
34
string
alt_loc_h
Alternate location indicator.
36
string
chain_h
Chain identifier.
37-41
int
res_seq_h
Residue sequence number.
42
string
ins_codeH
Insertion code.
44-47
string
name2
Atom name.
48
string
alt_loc2
Alternate location indicator.
49-51
string
res_name2
Residue name.
53
string
chain_id2
Chain identifier.
54-58
int
res_seq2
Residue sequence number.
59
string
ins_code2
Insertion code.
60-65
string
sym1
Symmetry operator for 1st non-hydrogen atom.
67-72
string
sym2
Symmetry operator for 2nd non-hydrogen atom.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.JRNL(line)[source]
JRNL field
The JRNL record contains the primary literature citation that describes the experiment which resulted in the deposited coordinate set. There is at most one JRNL reference per entry. If there is no primary reference, then there is no JRNL reference. Other references are given in REMARK 1.
- class pdb2pqr.pdb.KEYWDS(line)[source]
KEYWDS field
The KEYWDS record contains a set of terms relevant to the entry. Terms in the KEYWDS record provide a simple means of categorizing entries and may be used to generate index files. This record addresses some of the limitations found in the classification field of the HEADER record. It provides the opportunity to add further annotation to the entry in a concise and computer-searchable fashion.
- class pdb2pqr.pdb.LINK(line)[source]
LINK field
The LINK records specify connectivity between residues that is not implied by the primary structure. Connectivity is expressed in terms of the atom names. This record supplements information given in CONECT records and is provided here for convenience in searching.
- __init__(line)[source]
Initialize by parsing line
COLUMNS
TYPE
FIELD
DEFINITION
13-16
string
name1
Atom name.
17
string
alt_loc1
Alternate location indicator.
18-20
string
res_name1
Residue name.
22
string
chain_id1
Chain identifier.
23-26
int
res_seq1
Residue sequence number.
27
string
ins_code1
Insertion code.
43-46
string
name2
Atom name.
47
string
alt_loc2
Alternate location indicator.
48-50
string
res_name2
Residue name.
52
string
chain_id2
Chain identifier.
53-56
int
res_seq2
Residue sequence number.
57
string
ins_code2
Insertion code.
60-65
string
sym1
Symmetry operator for 1st atom.
67-72
string
sym2
Symmetry operator for 2nd atom.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.MASTER(line)[source]
MASTER class
The MASTER record is a control record for bookkeeping. It lists the number of lines in the coordinate entry or file for selected record types.
- __init__(line)[source]
Initialize by parsing line
COLUMNS
TYPE
FIELD
DEFINITION
11-15
int
num_remark
Number of REMARK records
21-25
int
num_het
Number of HET records
26-30
int
numHelix
Number of HELIX records
31-35
int
numSheet
Number of SHEET records
36-40
int
numTurn
Number of TURN records
41-45
int
numSite
Number of SITE records
46-50
int
numXform
Number of coordinate transformation records (ORIGX+SCALE+MTRIX)
51-55
int
numCoord
Number of atomic coordinate records (ATOM+HETATM)
56-60
int
numTer
Number of TER records
61-65
int
numConect
Number of CONECT records
66-70
int
numSeq
Number of SEQRES records
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.MODEL(line)[source]
MODEL class
The MODEL record specifies the model serial number when multiple structures are presented in a single coordinate entry, as is often the case with structures determined by NMR.
- class pdb2pqr.pdb.MODRES(line)[source]
MODRES field
The MODRES record provides descriptions of modifications (e.g., chemical or post-translational) to protein and nucleic acid residues. Included are a mapping between residue names given in a PDB entry and standard residues.
- __init__(line)[source]
Initialize by parsing a line
COLUMNS
TYPE
FIELD
DEFINITION
8-11
string
id_code
ID code of this entry.
13-15
string
res_name
Residue name used in this entry.
17
string
chain_id
Chain identifier.
19-22
int
seq_num
Sequence number.
23
string
ins_code
Insertion code.
25-27
string
stdRes
Standard residue name.
30-70
string
comment
Description of the residue modification.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.MTRIXn(line)[source]
MTRIXn baseclass
The MTRIXn (n = 1, 2, or 3) records present transformations expressing non-crystallographic symmetry.
- __init__(line)[source]
Initialize by parsing line
COLUMNS
TYPE
FIELD
DEFINITION
8-10
int
serial
Serial number
11-20
float
mn1
M31
21-30
float
mn2
M32
31-40
float
mn3
M33
46-55
float
vn
V3
60
int
i_given
1 if coordinates for the representations which are approximately related by the transformations of the molecule are contained in the entry. Otherwise, blank.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.NUMMDL(line)[source]
NUMMDL class
The NUMMDL record indicates total number of models in a PDB entry.
- class pdb2pqr.pdb.OBSLTE(line)[source]
OBSLTE field
This record acts as a flag in an entry which has been withdrawn from the PDB’s full release. It indicates which, if any, new entries have replaced the withdrawn entry.
The format allows for the case of multiple new entries replacing one existing entry.
- __init__(line)[source]
Initialize by parsing a line.
COLUMNS
TYPE
FIELD
DEFINITION
12-20
string
replace_date
Date that this entry was replaced.
22-25
string
id_code
ID code of this entry.
32-35
string
rid_code
ID code of entry that replaced this one.
37-40
string
rid_code
ID code of entry that replaced this one.
42-45
string
rid_code
ID code of entry that replaced this one.
47-50
string
rid_code
ID code of entry that replaced this one.
52-55
string
rid_code
ID code of entry that replaced this one.
57-60
string
rid_code
ID code of entry that replaced this one.
62-65
string
rid_code
ID code of entry that replaced this one.
67-70
string
rid_code
ID code of entry that replaced this one.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.ORIGXn(line)[source]
ORIGXn class
The ORIGXn (n = 1, 2, or 3) records present the transformation from the orthogonal coordinates contained in the entry to the submitted coordinates.
- class pdb2pqr.pdb.REMARK(line)[source]
REMARK field
REMARK records present experimental details, annotations, comments, and information not included in other records. In a number of cases, REMARKs are used to expand the contents of other record types. A new level of structure is being used for some REMARK records. This is expected to facilitate searching and will assist in the conversion to a relational database.
- class pdb2pqr.pdb.REVDAT(line)[source]
REVDAT field
REVDAT records contain a history of the modifications made to an entry since its release.
- __init__(line)[source]
Initialize by parsing a line.
Todo
If multiple modifications are present, only the last one in the file is preserved.
COLUMNS
TYPE
FIELD
DEFINITION
8-10
int
mod_num
Modification number.
14-22
string
mod_date
Date of modification (or release for new entries).
24-28
string
mod_id
Identifies this particular modification. It links to the archive used internally by PDB.
32
int
mod_type
An integer identifying the type of modification. In case of revisions with more than one possible mod_type, the highest value applicable will be assigned.
40-45
string
record
Name of the modified record.
47-52
string
record
Name of the modified record.
54-59
string
record
Name of the modified record.
61-66
string
record
Name of the modified record.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.SCALEn(line)[source]
SCALEn baseclass
The SCALEn (n = 1, 2, or 3) records present the transformation from the orthogonal coordinates as contained in the entry to fractional crystallographic coordinates. Non-standard coordinate systems should be explained in the remarks.
- class pdb2pqr.pdb.SEQADV(line)[source]
SEQADV field
The SEQADV record identifies conflicts between sequence information in the ATOM records of the PDB entry and the sequence database entry given on DBREF. Please note that these records were designed to identify differences and not errors. No assumption is made as to which database contains the correct data. PDB may include REMARK records in the entry that reflect the depositor’s view of which database has the correct sequence.
- __init__(line)[source]
Initialize by parsing line
COLUMNS
TYPE
FIELD
DEFINITION
8-11
string
id_code
ID code of this entry.
13-15
string
res_name
Name of the PDB residue in conflict.
17
string
chain_id
PDB chain identifier.
19-22
int
seq_num
PDB sequence number.
23
string
ins_code
PDB insertion code.
25-28
string
database
Sequence database name.
30-38
string
db_id_code
Sequence database accession number.
40-42
string
db_res
Sequence database residue name.
44-48
int
db_seq
Sequence database sequence number.
50-70
string
conflict
Conflict comment.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.SEQRES(line)[source]
SEQRES field
SEQRES records contain the amino acid or nucleic acid sequence of residues in each chain of the macromolecule that was studied.
- __init__(line)[source]
Initialize by parsing a line
COLUMNS
TYPE
FIELD
DEFINITION
9-10
int
ser_num
Serial number of the SEQRES record for the current chain. Starts at 1 and increments by one each line. Reset to 1 for each chain.
12
string
chain_id
Chain identifier. This may be any single legal character, including a blank which is used if there is only one chain.
14-17
int
num_res
Number of residues in the chain. This value is repeated on every record.
20-22
string
res_name
Residue name.
24-26
string
res_name
Residue name.
28-30
string
res_name
Residue name.
32-34
string
res_name
Residue name.
36-38
string
res_name
Residue name.
40-42
string
res_name
Residue name.
44-46
string
res_name
Residue name.
48-50
string
res_name
Residue name.
52-54
string
res_name
Residue name.
56-58
string
res_name
Residue name.
60-62
string
res_name
Residue name.
64-66
string
res_name
Residue name.
68-70
string
res_name
Residue name.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.SHEET(line)[source]
SHEET field
SHEET records are used to identify the position of sheets in the molecule. Sheets are both named and numbered. The residues where the sheet begins and ends are noted.
- __init__(line)[source]
Initialize by parsing line
COLUMNS
TYPE
FIELD
DEFINITION
8-10
int
strand
Strand number which starts at 1 for each strand within a sheet and increases by one.
12-14
string
sheet_id
Sheet identifier.
15-16
int
num_strands
Number of strands in sheet.
18-20
string
init_res_name
Residue name of initial residue.
22
string
init_chain_id
Chain identifier of initial residue in strand.
23-26
int
init_seq_num
Sequence number of initial residue in strand.
27
string
init_i_code
Insertion code of initial residue in strand.
29-31
string
end_res_name
Residue name of terminal residue.
33
string
end_chain_id
Chain identifier of terminal residue.
34-37
int
end_seq_num
Sequence number of terminal residue.
38
string
end_i_code
Insertion code of terminal residue.
39-40
int
sense
Sense of strand with respect to previous strand in the sheet. 0 if first strand, 1 if parallel, -1 if anti-parallel.
42-45
string
cur_atom
Registration. Atom name in current strand.
46-48
string
curr_res_name
Registration. Residue name in current strand.
50
string
curChainId
Registration. Chain identifier in current strand.
51-54
int
curr_res_seq
Registration. Residue sequence number in current strand.
55
string
curr_ins_code
Registration. Insertion code in current strand.
57-60
string
prev_atom
Registration. Atom name in previous strand.
61-63
string
prev_res_name
Registration. Residue name in previous strand.
65
string
prevChainId
Registration. Chain identifier in previous strand.
66-69
int
prev_res_seq
Registration. Residue sequence number in previous strand.
70
string
prev_ins_code
Registration. Insertion code in previous strand.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.SIGATM(line)[source]
SIGATM class
The SIGATM records present the standard deviation of atomic parameters as they appear in ATOM and HETATM records.
- __init__(line)[source]
Initialize by parsing line
COLUMNS
TYPE
FIELD
DEFINITION
7-11
int
serial
Atom serial number.
13-16
string
name
Atom name.
17
string
alt_loc
Alternate location indicator.
18-20
string
res_name
Residue name.
22
string
chain_id
Chain identifier.
23-26
int
res_seq
Residue sequence number.
27
string
ins_code
Code for insertion of residues.
31-38
float
sig_x
Standard deviation of orthogonal coordinates for X in Angstroms.
39-46
float
sig_y
Standard deviation of orthogonal coordinates for Y in Angstroms.
47-54
float
sig_z
Standard deviation of orthogonal coordinates for Z in Angstroms.
55-60
float
sig_occ
Standard deviation of occupancy.
61-66
float
sig_temp
Standard deviation of temperature factor.
73-76
string
seg_id
Segment identifier, left-justified.
77-78
string
element
Element symbol, right-justified.
79-80
string
charge
Charge on the atom.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.SIGUIJ(line)[source]
SIGUIJ class
The SIGUIJ records present the anisotropic temperature factors.
- __init__(line)[source]
Initialize by parsing line:
COLUMNS
TYPE
FIELD
DEFINITION
7-11
int
serial
Atom serial number.
13-16
string
name
Atom name.
17
string
alt_loc
Alternate location indicator.
18-20
string
res_name
Residue name.
22
string
chain_id
Chain identifier.
23-26
int
res_seq
Residue sequence number.
27
string
ins_code
Insertion code.
29-35
int
sig11
Sigma U(1,1)
36-42
int
sig22
Sigma U(2,2)
43-49
int
sig33
Sigma U(3,3)
50-56
int
sig12
Sigma U(1,2)
57-63
int
sig13
Sigma U(1,3)
64-70
int
sig23
Sigma U(2,3)
73-76
string
seg_id
Segment identifier, left-justified.
77-78
string
el.ment
Element symbol, right-justified.
79-80
string
charge
Charge on the atom.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.SITE(line)[source]
SITE class
The SITE records supply the identification of groups comprising important sites in the macromolecule.
- __init__(line)[source]
Initialize by parsing the line
COLUMNS 8-10
TYPE int
FIELD seq_num
DEFINITION Sequence number.
12-14
string
site_id
Site name.
16-17
int
num_res
Number of residues comprising site.
19-21
string
res_name1
Residue name for first residue comprising site.
23
string
chain_id1
Chain identifier for first residue comprising site.
24-27
int
seq1
Residue sequence number for first residue comprising site.
28
string
ins_code1
Insertion code for first residue comprising site.
30-32
string
res_name2
Residue name for second residue comprising site.
34
string
chain_id2
Chain identifier for second residue comprising site.
35-38
int
seq2
Residue sequence number for second residue comprising site.
39
string
ins_code2
Insertion code for second residue comprising site.
41-43
string
res_name3
Residue name for third residue comprising site.
45
string
chain_id3
Chain identifier for third residue comprising site.
46-49
int
seq3
Residue sequence number for third residue comprising site.
50
string
ins_code3
Insertion code for third residue comprising site.
52-54
string
res_name4
Residue name for fourth residue comprising site.
56
string
chain_id4
Chain identifier for fourth residue comprising site.
57-60
int
seq4
Residue sequence number for fourth residue comprising site.
61
string
ins_code4
Insertion code for fourth residue comprising site.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.SLTBRG(line)[source]
SLTBRG field
The SLTBRG records specify salt bridges in the entry. records and is provided here for convenience in searching.
- __init__(line)[source]
Initialize by parsing line
COLUMNS
TYPE
FIELD
DEFINITION
13-16
string
name1
Atom name.
17
string
alt_loc1
Alternate location indicator.
18-20
string
res_name1
Residue name.
22
string
chain_id1
Chain identifier.
23-26
int
res_seq1
Residue sequence number.
27
string
ins_code1
Insertion code.
43-46
string
name2
Atom name.
47
string
alt_loc2
Alternate location indicator.
48-50
string
res_name2
Residue name.
52
string
chain_id2
Chain identifier.
53-56
int
res_seq2
Residue sequence number.
57
string
ins_code2
Insertion code.
60-65
string
sym1
Symmetry operator for 1st atom.
67-72
string
sym2
Symmetry operator for 2nd atom.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.SOURCE(line)[source]
SOURCE field
The SOURCE record specifies the biological and/or chemical source of each biological molecule in the entry. Sources are described by both the common name and the scientific name, e.g., genus and species. Strain and/or cell-line for immortalized cells are given when they help to uniquely identify the biological entity studied.
- class pdb2pqr.pdb.SPRSDE(line)[source]
SPRSDE field
The SPRSDE records contain a list of the ID codes of entries that were made obsolete by the given coordinate entry and withdrawn from the PDB release set. One entry may replace many. It is PDB policy that only the principal investigator of a structure has the authority to withdraw it.
- __init__(line)[source]
Initialize by parsing line
COLUMNS
TYPE
FIELD
DEFINITION
12-20
string
super_date
Date this entry superseded the listed entries.
22-25
string
id_code
ID code of this entry.
32-35
string
sid_code
ID code of a superseded entry.
37-40
string
sid_code
ID code of a superseded entry.
42-45
string
sid_code
ID code of a superseded entry.
47-50
string
sid_code
ID code of a superseded entry.
52-55
string
sid_code
ID code of a superseded entry.
57-60
string
sid_code
ID code of a superseded entry.
62-65
string
sid_code
ID code of a superseded entry.
67-70
string
sid_code
ID code of a superseded entry.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.SSBOND(line)[source]
SSBOND field
The SSBOND record identifies each disulfide bond in protein and polypeptide structures by identifying the two residues involved in the bond.
- __init__(line)[source]
Initialize by parsing line
COLUMNS
TYPE
FIELD
DEFINITION
8-10
int
ser_num
Serial number.
16
string
chain_id1
Chain identifier.
18-21
int
seq_num1
Residue sequence number.
22
string
icode1
Insertion code.
30
string
chain_id2
Chain identifier.
32-35
int
seq_num2
Residue sequence number.
36
string
icode2
Insertion code.
60-65
string
sym1
Symmetry operator for 1st residue.
67-72
string
sym2
Symmetry operator for 2nd residue.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.TER(line)[source]
TER class
The TER record indicates the end of a list of ATOM/HETATM records for a chain.
- __init__(line)[source]
Initialize by parsing line:
COLUMNS
TYPE
FIELD
DEFINITION
7-11
int
serial
Serial number.
18-20
string
res_name
Residue name.
22
string
chain_id
Chain identifier.
23-26
int
res_seq
Residue sequence number.
27
string
ins_code
Insertion code.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.TITLE(line)[source]
TITLE field
The TITLE record contains a title for the experiment or analysis that is represented in the entry. It should identify an entry in the PDB in the same way that a title identifies a paper.
- class pdb2pqr.pdb.TURN(line)[source]
TURN field
The TURN records identify turns and other short loop turns which normally connect other secondary structure segments.
- __init__(line)[source]
Initialize by parsing line
COLUMNS
TYPE
FIELD
DEFINITION
8-10
int
seq
Turn number; starts with 1 and increments by one.
12-14
string
turn_id
Turn identifier.
16-18
string
init_res_name
Residue name of initial residue in turn.
20
string
init_chain_id
Chain identifier for the chain containing this turn.
21-24
int
init_seq_num
Sequence number of initial residue in turn.
25
string
init_i_code
Insertion code of initial residue in turn.
27-29
string
end_res_name
Residue name of terminal residue of turn.
31
string
end_chain_id
Chain identifier for the chain containing this turn.
32-35
int
end_seq_num
Sequence number of terminal residue of turn.
36
string
end_i_code
Insertion code of terminal residue of turn.
41-70
string
comment
Associated comment.
- Parameters:
line (str) – line with PDB class
- class pdb2pqr.pdb.TVECT(line)[source]
TVECT class
The TVECT records present the translation vector for infinite covalently connected structures.
- __init__(line)[source]
Initialize by parsing line
COLUMNS
TYPE
FIELD
DEFINITION
8-10
int
serial
Serial number
11-20
float
t1
Components of translation vector
21-30
float
t2
Components of translation vector
31-40
float
t2
Components of translation vector
41-70
string
text
Comments
- Parameters:
line (str) – line with PDB class
- pdb2pqr.pdb.read_atom(line)[source]
If the ATOM/HETATM is not column-formatted, try to get some information by parsing whitespace from the right. Look for five floating point numbers followed by the residue number.
- Parameters:
line (str) – the line to parse